Is shell=True ever acceptable

When the command genuinely is a shell pipeline you control end to end, and never with any value that came from outside the program. The list form avoids quoting entirely, which is both safer and easier to read.

Keep the work in functions, put argument parsing in main(), and guard with if __name__ == "__main__": sys.exit(main()). Return codes from main then work for both the shell and the tests.

When you stop noticing it. If it has not surfaced a problem in six months, it is either solved or it was never the bottleneck you thought.